From c69038ebf477188886858c36974ba1c8f471a1d2 Mon Sep 17 00:00:00 2001 From: blancoapa Date: Wed, 8 May 2024 15:12:08 +0200 Subject: [PATCH] clean-up output from tutorials --- tutorials/pyMBE_tutorial.ipynb | 1548 ++--------------------------- tutorials/solution_tutorial.ipynb | 23 +- 2 files changed, 66 insertions(+), 1505 deletions(-) diff --git a/tutorials/pyMBE_tutorial.ipynb b/tutorials/pyMBE_tutorial.ipynb index 2e6be2b..b12d7b3 100644 --- a/tutorials/pyMBE_tutorial.ipynb +++ b/tutorials/pyMBE_tutorial.ipynb @@ -42,7 +42,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -65,7 +65,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -87,23 +87,9 @@ }, { "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\n", - "Current set of reduced units:\n", - "0.355 nanometer = 1 reduced_length\n", - "4.11640356238e-21 joule = 1 reduced_energy\n", - "Temperature: 298.15 kelvin\n", - "1.602176634e-19 coulomb = 1 reduced_charge\n", - "\n" - ] - } - ], + "execution_count": null, + "metadata": {}, + "outputs": [], "source": [ "pmb.print_reduced_units()" ] @@ -117,23 +103,9 @@ }, { "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\n", - "Current set of reduced units:\n", - "0.49999999999999994 nanometer = 1 reduced_length\n", - "4.11640356238e-21 joule = 1 reduced_energy\n", - "Temperature: 298.15 kelvin\n", - "8.01088317e-19 coulomb = 1 reduced_charge\n", - "\n" - ] - } - ], + "execution_count": null, + "metadata": {}, + "outputs": [], "source": [ "pmb.set_reduced_units(unit_length = 0.5*pmb.units.nm, \n", " unit_charge = 5*pmb.units.e)\n", @@ -156,17 +128,9 @@ }, { "cell_type": "code", - "execution_count": 5, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "The side of the simulation box is 7.5 nanometer = 14.999999999999998 reduced_length\n" - ] - } - ], + "execution_count": null, + "metadata": {}, + "outputs": [], "source": [ "Box_L = 7.5*pmb.units.nm\n", "\n", @@ -191,7 +155,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -211,86 +175,9 @@ }, { "cell_type": "code", - "execution_count": 7, - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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labeles_typecharge
0BB-PDhaparticle000inert0.4 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyBB-PDha00
1COOH-PDhaparticle100inert0.5 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyCOOH-PDha10
2NH3-PDhaparticle200inert0.3 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyNH3-PDha20
9BB-PDhaparticle310inert0.4 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyBB-PDha00
10COOH-PDhaparticle410inert0.5 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyCOOH-PDha10
12NH3-PDhaparticle510inert0.3 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyNH3-PDha20
15BB-PDhaparticle620inert0.4 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyBB-PDha00
16COOH-PDhaparticle720inert0.5 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyCOOH-PDha10
18NH3-PDhaparticle820inert0.3 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyNH3-PDha20
21BB-PDhaparticle930inert0.4 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyBB-PDha00
22COOH-PDhaparticle1030inert0.5 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyCOOH-PDha10
24NH3-PDhaparticle1130inert0.3 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyNH3-PDha20
28BB-PDhaparticle1240inert0.4 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyBB-PDha00
29COOH-PDhaparticle1340inert0.5 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyCOOH-PDha10
31NH3-PDhaparticle1440inert0.3 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyNH3-PDha20
35BB-PDhaparticle1550inert0.4 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyBB-PDha00
36COOH-PDhaparticle1650inert0.5 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyCOOH-PDha10
38NH3-PDhaparticle1750inert0.3 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyNH3-PDha20
42BB-PDhaparticle1860inert0.4 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyBB-PDha00
43COOH-PDhaparticle1960inert0.5 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyCOOH-PDha10
45NH3-PDhaparticle2060inert0.3 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyNH3-PDha20
49BB-PDhaparticle2170inert0.4 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyBB-PDha00
50COOH-PDhaparticle2270inert0.5 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyCOOH-PDha10
52NH3-PDhaparticle2370inert0.3 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyNH3-PDha20
56BB-PDhaparticle2480inert0.4 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyBB-PDha00
57COOH-PDhaparticle2580inert0.5 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyCOOH-PDha10
59NH3-PDhaparticle2680inert0.3 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyNH3-PDha20
63BB-PDhaparticle2790inert0.4 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyBB-PDha00
64COOH-PDhaparticle2890inert0.5 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyCOOH-PDha10
66NH3-PDhaparticle2990inert0.3 nanometer1.122462048309373 reduced_length0 reduced_length1 reduced_energyNH3-PDha20
\n", - "
" - ], - "text/plain": [ - " name pmb_type particle_id residue_id molecule_id acidity \\\n", - " \n", - "0 BB-PDha particle 0 0 0 inert \n", - "1 COOH-PDha particle 1 0 0 inert \n", - "2 NH3-PDha particle 2 0 0 inert \n", - "9 BB-PDha particle 3 1 0 inert \n", - "10 COOH-PDha particle 4 1 0 inert \n", - "12 NH3-PDha particle 5 1 0 inert \n", - "15 BB-PDha particle 6 2 0 inert \n", - "16 COOH-PDha particle 7 2 0 inert \n", - "18 NH3-PDha particle 8 2 0 inert \n", - "21 BB-PDha particle 9 3 0 inert \n", - "22 COOH-PDha particle 10 3 0 inert \n", - "24 NH3-PDha particle 11 3 0 inert \n", - "28 BB-PDha particle 12 4 0 inert \n", - "29 COOH-PDha particle 13 4 0 inert \n", - "31 NH3-PDha particle 14 4 0 inert \n", - "35 BB-PDha particle 15 5 0 inert \n", - "36 COOH-PDha particle 16 5 0 inert \n", - "38 NH3-PDha particle 17 5 0 inert \n", - "42 BB-PDha particle 18 6 0 inert \n", - "43 COOH-PDha particle 19 6 0 inert \n", - "45 NH3-PDha particle 20 6 0 inert \n", - "49 BB-PDha particle 21 7 0 inert \n", - "50 COOH-PDha particle 22 7 0 inert \n", - "52 NH3-PDha particle 23 7 0 inert \n", - "56 BB-PDha particle 24 8 0 inert \n", - "57 COOH-PDha particle 25 8 0 inert \n", - "59 NH3-PDha particle 26 8 0 inert \n", - "63 BB-PDha particle 27 9 0 inert \n", - "64 COOH-PDha particle 28 9 0 inert \n", - "66 NH3-PDha particle 29 9 0 inert \n", - "\n", - " sigma cutoff offset \\\n", - " \n", - "0 0.4 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", - "1 0.5 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", - "2 0.3 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", - "9 0.4 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", - "10 0.5 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", - "12 0.3 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", - "15 0.4 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", - "16 0.5 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", - "18 0.3 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", - "21 0.4 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", - "22 0.5 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", - "24 0.3 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", - "28 0.4 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", - "29 0.5 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", - "31 0.3 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", - "35 0.4 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", - "36 0.5 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", - "38 0.3 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", - "42 0.4 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", - "43 0.5 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", - "45 0.3 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", - "49 0.4 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", - "50 0.5 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", - "52 0.3 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", - "56 0.4 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", - "57 0.5 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", - "59 0.3 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", - "63 0.4 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", - "64 0.5 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", - "66 0.3 nanometer 1.122462048309373 reduced_length 0 reduced_length \n", - "\n", - " epsilon state_one \n", - " label es_type charge \n", - "0 1 reduced_energy BB-PDha 0 0 \n", - "1 1 reduced_energy COOH-PDha 1 0 \n", - "2 1 reduced_energy NH3-PDha 2 0 \n", - "9 1 reduced_energy BB-PDha 0 0 \n", - "10 1 reduced_energy COOH-PDha 1 0 \n", - "12 1 reduced_energy NH3-PDha 2 0 \n", - "15 1 reduced_energy BB-PDha 0 0 \n", - "16 1 reduced_energy COOH-PDha 1 0 \n", - "18 1 reduced_energy NH3-PDha 2 0 \n", - "21 1 reduced_energy BB-PDha 0 0 \n", - "22 1 reduced_energy COOH-PDha 1 0 \n", - "24 1 reduced_energy NH3-PDha 2 0 \n", - "28 1 reduced_energy BB-PDha 0 0 \n", - "29 1 reduced_energy COOH-PDha 1 0 \n", - "31 1 reduced_energy NH3-PDha 2 0 \n", - "35 1 reduced_energy BB-PDha 0 0 \n", - "36 1 reduced_energy COOH-PDha 1 0 \n", - "38 1 reduced_energy NH3-PDha 2 0 \n", - "42 1 reduced_energy BB-PDha 0 0 \n", - "43 1 reduced_energy COOH-PDha 1 0 \n", - "45 1 reduced_energy NH3-PDha 2 0 \n", - "49 1 reduced_energy BB-PDha 0 0 \n", - "50 1 reduced_energy COOH-PDha 1 0 \n", - "52 1 reduced_energy NH3-PDha 2 0 \n", - "56 1 reduced_energy BB-PDha 0 0 \n", - "57 1 reduced_energy COOH-PDha 1 0 \n", - "59 1 reduced_energy NH3-PDha 2 0 \n", - "63 1 reduced_energy BB-PDha 0 0 \n", - "64 1 reduced_energy COOH-PDha 1 0 \n", - "66 1 reduced_energy NH3-PDha 2 0 " - ] - }, - "execution_count": 18, - "metadata": {}, - "output_type": "execute_result" - } - ], + "execution_count": null, + "metadata": {}, + "outputs": [], "source": [ "pmb.filter_df(pmb_type = 'particle')" ] @@ -1639,7 +442,7 @@ }, { "cell_type": "code", - "execution_count": 19, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -1659,45 +462,9 @@ }, { "cell_type": "code", - "execution_count": 20, - "metadata": {}, - "outputs": [ - { - "data": { - "text/html": [ - "
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CA 0 0 \n", - "1 inert NaN NaN NaN ... D 1 None \n", - "2 inert NaN NaN NaN ... E 2 None \n", - "3 inert NaN NaN NaN ... H 3 None \n", - "4 inert NaN NaN NaN ... Y 4 None \n", - "5 inert NaN NaN NaN ... K 5 None \n", - "6 NaN NaN NaN NaN ... NaN NaN NaN \n", - "7 NaN NaN NaN NaN ... NaN NaN NaN \n", - "8 NaN NaN NaN NaN ... NaN NaN NaN \n", - "9 NaN NaN NaN NaN ... NaN NaN NaN \n", - "10 NaN NaN NaN NaN ... NaN NaN NaN \n", - "11 NaN NaN NaN NaN ... NaN NaN NaN \n", - "12 NaN NaN CA [K] ... NaN NaN NaN \n", - "13 NaN NaN CA [E] ... NaN NaN NaN \n", - "14 NaN NaN NaN NaN ... NaN NaN NaN \n", - "\n", - " state_two sequence \\\n", - " label es_type charge \n", - "0 NaN NaN NaN NaN \n", - "1 NaN NaN NaN NaN \n", - "2 NaN NaN NaN NaN \n", - "3 NaN NaN NaN NaN \n", - "4 NaN NaN NaN NaN \n", - "5 NaN NaN NaN NaN \n", - "6 NaN NaN NaN NaN \n", - "7 NaN NaN NaN NaN \n", - "8 NaN NaN NaN NaN \n", - "9 NaN NaN NaN NaN \n", - "10 NaN NaN NaN NaN \n", - "11 NaN NaN NaN NaN \n", - "12 NaN NaN NaN NaN \n", - "13 NaN NaN NaN NaN \n", - "14 NaN NaN NaN [K, K, K, K, K, E, E, E, E, E] \n", - "\n", - " bond_object \\\n", - " \n", - "0 NaN \n", - "1 NaN \n", - "2 NaN \n", - "3 NaN \n", - "4 NaN \n", - "5 NaN \n", - "6 HarmonicBond({'r_cut': 0.0, 'k': 99.9999999999... \n", - "7 HarmonicBond({'r_cut': 0.0, 'k': 99.9999999999... \n", - "8 HarmonicBond({'r_cut': 0.0, 'k': 99.9999999999... \n", - "9 HarmonicBond({'r_cut': 0.0, 'k': 99.9999999999... \n", - "10 HarmonicBond({'r_cut': 0.0, 'k': 99.9999999999... \n", - "11 HarmonicBond({'r_cut': 0.0, 'k': 99.9999999999... \n", - "12 NaN \n", - "13 NaN \n", - "14 NaN \n", - "\n", - " parameters_of_the_potential l0 \n", - " \n", - "0 NaN NaN \n", - "1 NaN NaN \n", - "2 NaN NaN \n", - "3 NaN NaN \n", - "4 NaN NaN \n", - "5 NaN NaN \n", - "6 {'k': 99.99999999999999, 'r_cut': 0.0, 'r_0': ... 0.776371 \n", - "7 {'k': 99.99999999999999, 'r_cut': 0.0, 'r_0': ... 0.744156 \n", - "8 {'k': 99.99999999999999, 'r_cut': 0.0, 'r_0': ... 0.870000 \n", - "9 {'k': 99.99999999999999, 'r_cut': 0.0, 'r_0': ... 0.904000 \n", - "10 {'k': 99.99999999999999, 'r_cut': 0.0, 'r_0': ... 1.296000 \n", - "11 {'k': 99.99999999999999, 'r_cut': 0.0, 'r_0': ... 1.116000 \n", - "12 NaN NaN \n", - "13 NaN NaN \n", - "14 NaN NaN \n", - "\n", - "[15 rows x 26 columns]\n" - ] - } - ], + "execution_count": null, + "metadata": {}, + "outputs": [], "source": [ "print(pmb.df)" ] @@ -2499,30 +1096,9 @@ }, { "cell_type": "code", - "execution_count": 37, - "metadata": {}, - "outputs": [ - { - "ename": "ValueError", - "evalue": "Charge has to be a float. -- Got an NoneType", - "output_type": "error", - "traceback": [ - "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", - "\u001b[0;31mValueError\u001b[0m Traceback (most recent call last)", - "Cell \u001b[0;32mIn[37], line 5\u001b[0m\n\u001b[1;32m 1\u001b[0m pmb\u001b[38;5;241m.\u001b[39mdefine_peptide(name \u001b[38;5;241m=\u001b[39m sequence, \n\u001b[1;32m 2\u001b[0m sequence \u001b[38;5;241m=\u001b[39m sequence, \n\u001b[1;32m 3\u001b[0m model \u001b[38;5;241m=\u001b[39m model)\n\u001b[0;32m----> 5\u001b[0m \u001b[43mpmb\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcreate_pmb_object\u001b[49m\u001b[43m(\u001b[49m\u001b[43mname\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[43msequence\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 6\u001b[0m \u001b[43m \u001b[49m\u001b[43mnumber_of_objects\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[43mN_peptide\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 7\u001b[0m \u001b[43m \u001b[49m\u001b[43mespresso_system\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[43mespresso_system\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 8\u001b[0m \u001b[43m \u001b[49m\u001b[43mposition\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[43m[\u001b[49m\u001b[43m[\u001b[49m\u001b[43mBox_L\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mto\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mreduced_length\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m)\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mmagnitude\u001b[49m\u001b[38;5;241;43m/\u001b[39;49m\u001b[38;5;241;43m2\u001b[39;49m\u001b[43m]\u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m3\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m)\u001b[49m\n", - "File \u001b[0;32m~/Desktop/pyMBE_jn/pyMBE.py:1009\u001b[0m, in \u001b[0;36mpymbe_library.create_pmb_object\u001b[0;34m(self, name, number_of_objects, espresso_system, position, use_default_bond)\u001b[0m\n\u001b[1;32m 1007\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mcreate_residue(name\u001b[38;5;241m=\u001b[39mname, number_of_residues\u001b[38;5;241m=\u001b[39mnumber_of_objects, espresso_system\u001b[38;5;241m=\u001b[39mespresso_system, central_bead_position\u001b[38;5;241m=\u001b[39mposition,use_default_bond\u001b[38;5;241m=\u001b[39muse_default_bond)\n\u001b[1;32m 1008\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m pmb_type \u001b[38;5;241m==\u001b[39m \u001b[38;5;124m'\u001b[39m\u001b[38;5;124mmolecule\u001b[39m\u001b[38;5;124m'\u001b[39m:\n\u001b[0;32m-> 1009\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcreate_molecule\u001b[49m\u001b[43m(\u001b[49m\u001b[43mname\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mname\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mnumber_of_molecules\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mnumber_of_objects\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mespresso_system\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mespresso_system\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43muse_default_bond\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43muse_default_bond\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mlist_of_first_residue_positions\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mposition\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1010\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m\n", - "File \u001b[0;32m~/Desktop/pyMBE_jn/pyMBE.py:884\u001b[0m, in \u001b[0;36mpymbe_library.create_molecule\u001b[0;34m(self, name, number_of_molecules, espresso_system, list_of_first_residue_positions, use_default_bond)\u001b[0m\n\u001b[1;32m 879\u001b[0m \u001b[38;5;66;03m# Generate an arbitrary random unit vector\u001b[39;00m\n\u001b[1;32m 880\u001b[0m backbone_vector \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgenerate_random_points_in_a_sphere(center\u001b[38;5;241m=\u001b[39m[\u001b[38;5;241m0\u001b[39m,\u001b[38;5;241m0\u001b[39m,\u001b[38;5;241m0\u001b[39m], \n\u001b[1;32m 881\u001b[0m radius\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m1\u001b[39m, \n\u001b[1;32m 882\u001b[0m n_samples\u001b[38;5;241m=\u001b[39m\u001b[38;5;241m1\u001b[39m,\n\u001b[1;32m 883\u001b[0m on_surface\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mTrue\u001b[39;00m)[\u001b[38;5;241m0\u001b[39m]\n\u001b[0;32m--> 884\u001b[0m residues_info \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcreate_residue\u001b[49m\u001b[43m(\u001b[49m\u001b[43mname\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mresidue\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 885\u001b[0m \u001b[43m \u001b[49m\u001b[43mnumber_of_residues\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\n\u001b[1;32m 886\u001b[0m \u001b[43m \u001b[49m\u001b[43mespresso_system\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mespresso_system\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\n\u001b[1;32m 887\u001b[0m \u001b[43m \u001b[49m\u001b[43mcentral_bead_position\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mresidue_position\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\n\u001b[1;32m 888\u001b[0m \u001b[43m \u001b[49m\u001b[43muse_default_bond\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[43muse_default_bond\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\n\u001b[1;32m 889\u001b[0m \u001b[43m \u001b[49m\u001b[43mbackbone_vector\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mbackbone_vector\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 890\u001b[0m residue_id \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mnext\u001b[39m(\u001b[38;5;28miter\u001b[39m(residues_info))\n\u001b[1;32m 891\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m index \u001b[38;5;129;01min\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdf[\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdf[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mresidue_id\u001b[39m\u001b[38;5;124m'\u001b[39m]\u001b[38;5;241m==\u001b[39mresidue_id]\u001b[38;5;241m.\u001b[39mindex:\n", - "File \u001b[0;32m~/Desktop/pyMBE_jn/pyMBE.py:1149\u001b[0m, in \u001b[0;36mpymbe_library.create_residue\u001b[0;34m(self, name, espresso_system, number_of_residues, central_bead_position, use_default_bond, backbone_vector)\u001b[0m\n\u001b[1;32m 1145\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 1146\u001b[0m bead_position\u001b[38;5;241m=\u001b[39mcentral_bead_position\u001b[38;5;241m+\u001b[39m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mgenerate_trial_perpendicular_vector(vector\u001b[38;5;241m=\u001b[39mbackbone_vector,\n\u001b[1;32m 1147\u001b[0m magnitude\u001b[38;5;241m=\u001b[39ml0)\n\u001b[0;32m-> 1149\u001b[0m side_bead_id \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcreate_particle\u001b[49m\u001b[43m(\u001b[49m\u001b[43mname\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mside_chain_element\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\n\u001b[1;32m 1150\u001b[0m \u001b[43m \u001b[49m\u001b[43mespresso_system\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mespresso_system\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 1151\u001b[0m \u001b[43m \u001b[49m\u001b[43mposition\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m[\u001b[49m\u001b[43mbead_position\u001b[49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\n\u001b[1;32m 1152\u001b[0m \u001b[43m \u001b[49m\u001b[43mnumber_of_particles\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m)\u001b[49m[\u001b[38;5;241m0\u001b[39m]\n\u001b[1;32m 1153\u001b[0m index \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdf[\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mdf[\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mparticle_id\u001b[39m\u001b[38;5;124m'\u001b[39m]\u001b[38;5;241m==\u001b[39mside_bead_id]\u001b[38;5;241m.\u001b[39mindex\u001b[38;5;241m.\u001b[39mvalues[\u001b[38;5;241m0\u001b[39m]\n\u001b[1;32m 1154\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39madd_value_to_df(key\u001b[38;5;241m=\u001b[39m(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mresidue_id\u001b[39m\u001b[38;5;124m'\u001b[39m,\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m'\u001b[39m),\n\u001b[1;32m 1155\u001b[0m index\u001b[38;5;241m=\u001b[39m\u001b[38;5;28mint\u001b[39m (index),\n\u001b[1;32m 1156\u001b[0m new_value\u001b[38;5;241m=\u001b[39mresidue_id, \n\u001b[1;32m 1157\u001b[0m verbose\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m)\n", - "File \u001b[0;32m~/Desktop/pyMBE_jn/pyMBE.py:982\u001b[0m, in \u001b[0;36mpymbe_library.create_particle\u001b[0;34m(self, name, espresso_system, number_of_particles, position, fix)\u001b[0m\n\u001b[1;32m 980\u001b[0m espresso_system\u001b[38;5;241m.\u001b[39mpart\u001b[38;5;241m.\u001b[39madd (\u001b[38;5;28mid\u001b[39m\u001b[38;5;241m=\u001b[39mbead_id, pos \u001b[38;5;241m=\u001b[39m particle_position, \u001b[38;5;28mtype\u001b[39m \u001b[38;5;241m=\u001b[39m es_type, q \u001b[38;5;241m=\u001b[39m q,fix \u001b[38;5;241m=\u001b[39m[fix,fix,fix]) \n\u001b[1;32m 981\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 982\u001b[0m \u001b[43mespresso_system\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mpart\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43madd\u001b[49m\u001b[43m \u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mid\u001b[39;49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mbead_id\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mpos\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[43mparticle_position\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43mtype\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[43mes_type\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mq\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43m \u001b[49m\u001b[43mq\u001b[49m\u001b[43m)\u001b[49m \n\u001b[1;32m 983\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39madd_value_to_df(key\u001b[38;5;241m=\u001b[39m(\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mparticle_id\u001b[39m\u001b[38;5;124m'\u001b[39m,\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m'\u001b[39m),index\u001b[38;5;241m=\u001b[39mdf_index,new_value\u001b[38;5;241m=\u001b[39mbead_id, verbose\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m) \n\u001b[1;32m 984\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m created_pid_list\n", - "File \u001b[0;32mparticle_data.pyx:1792\u001b[0m, in \u001b[0;36mespressomd.particle_data.ParticleList.add\u001b[0;34m()\u001b[0m\n", - "File \u001b[0;32mparticle_data.pyx:1834\u001b[0m, in \u001b[0;36mespressomd.particle_data.ParticleList._place_new_particle\u001b[0;34m()\u001b[0m\n", - "File \u001b[0;32mparticle_data.pyx:1446\u001b[0m, in \u001b[0;36mespressomd.particle_data.ParticleHandle.update\u001b[0;34m()\u001b[0m\n", - "File \u001b[0;32mparticle_data.pyx:578\u001b[0m, in \u001b[0;36mespressomd.particle_data.ParticleHandle.q.__set__\u001b[0;34m()\u001b[0m\n", - "File \u001b[0;32mutils.pyx:69\u001b[0m, in \u001b[0;36mespressomd.utils.check_type_or_throw_except\u001b[0;34m()\u001b[0m\n", - "\u001b[0;31mValueError\u001b[0m: Charge has to be a float. -- Got an NoneType" - ] - } - ], + "execution_count": null, + "metadata": {}, + "outputs": [], "source": [ "pmb.define_peptide(name = sequence, \n", " sequence = sequence, \n", diff --git a/tutorials/solution_tutorial.ipynb b/tutorials/solution_tutorial.ipynb index f40aeaf..07095be 100644 --- a/tutorials/solution_tutorial.ipynb +++ b/tutorials/solution_tutorial.ipynb @@ -28,24 +28,9 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": null, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "\n", - "Current set of reduced units:\n", - "1.5 nanometer = 1 reduced_length\n", - "4.11640356238e-21 joule = 1 reduced_energy\n", - "Temperature: 298.15 kelvin\n", - "8.01088317e-19 coulomb = 1 reduced_charge\n", - "\n", - "The side of the simulation box is 7.5 nanometer = 4.999999999999999 reduced_length\n" - ] - } - ], + "outputs": [], "source": [ "# Import pyMBE and ESPResSo\n", "import pyMBE\n", @@ -92,7 +77,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": null, "metadata": {}, "outputs": [], "source": [ @@ -259,7 +244,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.10" + "version": "3.10.12" }, "vscode": { "interpreter": {